dataAnnotatr <- read.csv(file.path(dataPath, dirO.7, "annotatr_results_E1_0.7.csv"))
allGenesDF <- data.frame(ENTREZID = dataAnnotatr$annot.gene_id,
SYMBOL = dataAnnotatr$annot.symbol)
# allGenesDF <- bitr(allGenes, fromType = "SYMBOL",
# toType = c("ENSEMBL", "ENTREZID"),
# OrgDb = org.Hs.eg.db)
ggo1 <- sapply(c("MF", "CC", "BP"), function(term) {
enrichGO(unique(allGenesDF$ENTREZID), org.Hs.eg.db,
ont = term, qvalueCutoff = 0.05,
readable = TRUE)})
dotplot(ggo1$MF, showCategory = 20, font.size = 8)
barplot(ggo1$MF, showCategory = 15, font.size = 9) + ggtitle("GO Molecular Function") +
theme(plot.title = element_text(face = "bold"))
ChIPseeker::upsetplot(ggo1$MF)
# upsetplot(ggo1$MF)
# goplot(ggo1)
barplot(ggo1$CC, showCategory = 10, font.size = 9) + ggtitle("GO Cellular Component") +
theme(plot.title = element_text(face = "bold"))
barplot(ggo1$BP, showCategory = 20, font.size = 9) + ggtitle("GO Biological Process") +
theme(plot.title = element_text(face = "bold"))
ggo1MFsimplified <- simplify(ggo1$MF)
dotplot(ggo1MFsimplified, showCategory = 20, font.size = 8)
barplot(ggo1MFsimplified, showCategory = 20, font.size = 8) + ggtitle("GO Molecular Function") +
theme(plot.title = element_text(face = "bold"))
kegg1 <- enrichKEGG(gene = allGenesDF$ENTREZID,
organism = "hsa")
dotplot(kegg1, showCategory = 20, font.size = 9) + ggtitle("KEGG pathways") +
theme(plot.title = element_text(face = "bold"))
barplot(kegg1, showCategory = 20, font.size = 9) + ggtitle("KEGG pathways") +
theme(plot.title = element_text(face = "bold"))
ChIPseeker::upsetplot(kegg1) + ggtitle("KEGG pathways") +
theme(plot.title = element_text(face = "bold"))
Link datos: http://bio-bigdata.hrbmu.edu.cn/CellMarker
dataHumanCells <- read.delim(file.path(analysisPath, "/data/Human_cell_markers.txt"))
dataHumanCells <- dataHumanCells %>% tidyr::unite("cellMarker", tissueType,
cancerType, cellName, sep=", ") %>%
dplyr::select(cellMarker, geneID) %>%
dplyr::mutate(geneID = strsplit(geneID, ', '))
typeCells <- enricher(unique(allGenesDF$ENTREZID), TERM2GENE = dataHumanCells,
pAdjustMethod = "fdr", minGSSize = 5, qvalueCutoff = 0.2)
dotplot(typeCells, showCategory = 10, font.size = 8)
barplot(typeCells, "GeneRatio", showCategory = 10, font.size = 9) + ggtitle("Enriquecimiento CellMarker") +
theme(plot.title = element_text(face = "bold"))
ChIPseeker::upsetplot(typeCells)
motifs <- msigdbr(species = "Homo sapiens", category = "C3")
geneImmSginature <- msigdbr(species = "Homo sapiens", category = "C7") %>%
dplyr::select(gs_name, entrez_gene)
immCells <- enricher(unique(allGenesDF$ENTREZID), TERM2GENE = geneImmSginature)
dotplot(immCells, showCategory = 10, font.size = 6)
barplot(immCells, "GeneRatio", showCategory = 10, font.size = 8) + ggtitle("Enriquecimiento MSigDB (C7)") +
theme(plot.title = element_text(face = "bold"))
ChIPseeker::upsetplot(immCells)
dso1 <- enrichDGN(allGenesDF$ENTREZID, readable = TRUE)
dotplot(dso1, showCategory = 20, font.size = 8)
barplot(dso1, showCategory = 20, font.size = 9) + ggtitle("Enriquecimiento MSigDB (C7)") +
theme(plot.title = element_text(face = "bold"))
ChIPseeker::upsetplot(dso1)